Limits...
Viroids: from genotype to phenotype just relying on RNA sequence and structural motifs.

Flores R, Serra P, Minoia S, Di Serio F, Navarro B - Front Microbiol (2012)

Bottom Line: As a consequence of two unique physical properties, small size and circularity, viroid RNAs do not code for proteins and thus depend on RNA sequence/structural motifs for interacting with host proteins that mediate their invasion, replication, spread, and circumvention of defensive barriers.Besides these most stable secondary structures, viroid RNAs alternatively adopt during replication transient metastable conformations containing elements of local higher-order structure, prominent among which are the hammerhead ribozymes catalyzing a key replicative step in the family Avsunviroidae, and certain conserved hairpins that also mediate replication steps in the family Pospiviroidae.Therefore, different RNA structures - either global or local - determine different functions, thus highlighting the need for in-depth structural studies on viroid RNAs.

View Article: PubMed Central - PubMed

Affiliation: Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC) Valencia, Spain.

ABSTRACT
As a consequence of two unique physical properties, small size and circularity, viroid RNAs do not code for proteins and thus depend on RNA sequence/structural motifs for interacting with host proteins that mediate their invasion, replication, spread, and circumvention of defensive barriers. Viroid genomes fold up on themselves adopting collapsed secondary structures wherein stretches of nucleotides stabilized by Watson-Crick pairs are flanked by apparently unstructured loops. However, compelling data show that they are instead stabilized by alternative non-canonical pairs and that specific loops in the rod-like secondary structure, characteristic of Potato spindle tuber viroid and most other members of the family Pospiviroidae, are critical for replication and systemic trafficking. In contrast, rather than folding into a rod-like secondary structure, most members of the family Avsunviroidae adopt multibranched conformations occasionally stabilized by kissing-loop interactions critical for viroid viability in vivo. Besides these most stable secondary structures, viroid RNAs alternatively adopt during replication transient metastable conformations containing elements of local higher-order structure, prominent among which are the hammerhead ribozymes catalyzing a key replicative step in the family Avsunviroidae, and certain conserved hairpins that also mediate replication steps in the family Pospiviroidae. Therefore, different RNA structures - either global or local - determine different functions, thus highlighting the need for in-depth structural studies on viroid RNAs.

No MeSH data available.


Related in: MedlinePlus

Hairpin I structures of the five type species of the family Pospiviroidae. This element of secondary structure is formed by the upper CCR strand and a flanking inverted repeat of PSTVd, HSVd, CCCVd, ASSVd, and CbVd-1 (Coleus blumei viroid 1). Red fonts indicate conserved nucleotides in structurally similar positions. Continuous and broken lines represent Watson–Crick and non-canonical base-pairs, respectively. Notice that the variability preserves the overall structure of hairpin I, including the terminal palindromic tetraloop, the adjacent 3-bp stem, and the long stem. Left inset, hairpin I of the wild-type CEVd variant used to transform A. thaliana (notice two co-variations with respect to PSTVd at the basis of the long stem). Reproduced with permission from Gas et al. (2007).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3376415&req=5

Figure 2: Hairpin I structures of the five type species of the family Pospiviroidae. This element of secondary structure is formed by the upper CCR strand and a flanking inverted repeat of PSTVd, HSVd, CCCVd, ASSVd, and CbVd-1 (Coleus blumei viroid 1). Red fonts indicate conserved nucleotides in structurally similar positions. Continuous and broken lines represent Watson–Crick and non-canonical base-pairs, respectively. Notice that the variability preserves the overall structure of hairpin I, including the terminal palindromic tetraloop, the adjacent 3-bp stem, and the long stem. Left inset, hairpin I of the wild-type CEVd variant used to transform A. thaliana (notice two co-variations with respect to PSTVd at the basis of the long stem). Reproduced with permission from Gas et al. (2007).

Mentions: The metastable conformations contain hairpins, prominent among which is hairpin I (HP I) formed by the upper CCR strand and the flanking imperfect repeats. The finding that the nucleotide variability between members of the family Pospiviroidae preserves HP I (Riesner et al., 1979; Visvader et al., 1985; Polivka et al., 1996) – including the capping palindromic tetraloop with the two central residues phylogenetically conserved, the adjacent 3-bp stem with its central pair also phylogenetically conserved, an internal symmetric loop of 1–3 nt in each strand presumably stabilized by non-canonical interactions (Gast et al., 1998), and a stem of 9–10 bp occasionally interrupted by a 1-nt symmetric or asymmetric internal loop (Visvader et al., 1985; Flores et al., 1997; Figure 2) – adds further support to this structural element serving as the basis for an important function in vivo. In agreement with this notion, results obtained with an in vivo system based in transgenic Arabidopsis thaliana lines expressing dimeric transcripts of CEVd, Apple scar skin viroid (ASSVd), and Hop stunt viroid (HSVd) – that mimic the replicative intermediates – have mapped the cleavage site of the (+) strands of these three viroids at the upper CCR strand (Daròs and Flores, 2004; Gas et al., 2007), in a position homologous to that proposed for PSTVd with an in vitro system (Baumstark et al., 1997). Moreover, as a consequence of the peculiar features of HP I (Figure 2), the corresponding sequence of di- or oligomeric RNAs can alternative form a long double-stranded structure with a GC-rich central region of 10 bp containing the cleavage sites. The adoption in vivo of this double-stranded structure, which would be the actual substrate for cleavage in line with an early proposal (Diener, 1986), could be facilitated by hairpin I. More specifically, during transcription of oligomeric (+) RNAs of the family Pospiviroidae, a kissing-loop interaction between the palindromic tetraloops of two consecutive hairpin I motifs (Figure 3A), paralleling the situation observed in retroviruses (Paillart et al., 2004), might start intramolecular dimerization and their stems then form a longer interstrand duplex (Gas et al., 2007; Figure 3B). Furthermore, the cleavage sites in the double-stranded structure leave two 3′-protruding nucleotides in each strand (Figure 3C), the hallmark of class III RNases that display a clear preference for substrates with a compact secondary structure, like viroids, and generate products with 5′-phosphomonoester and free 3′-hydroxyl termini (MacRae and Doudna, 2007). The monomeric linear CEV (+) strands that accumulate in A. thaliana transgenically expressing the corresponding dimeric transcripts have indeed these termini (Gas et al., 2008), the ligation of which, interestingly, occurs through a novel pathway.


Viroids: from genotype to phenotype just relying on RNA sequence and structural motifs.

Flores R, Serra P, Minoia S, Di Serio F, Navarro B - Front Microbiol (2012)

Hairpin I structures of the five type species of the family Pospiviroidae. This element of secondary structure is formed by the upper CCR strand and a flanking inverted repeat of PSTVd, HSVd, CCCVd, ASSVd, and CbVd-1 (Coleus blumei viroid 1). Red fonts indicate conserved nucleotides in structurally similar positions. Continuous and broken lines represent Watson–Crick and non-canonical base-pairs, respectively. Notice that the variability preserves the overall structure of hairpin I, including the terminal palindromic tetraloop, the adjacent 3-bp stem, and the long stem. Left inset, hairpin I of the wild-type CEVd variant used to transform A. thaliana (notice two co-variations with respect to PSTVd at the basis of the long stem). Reproduced with permission from Gas et al. (2007).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3376415&req=5

Figure 2: Hairpin I structures of the five type species of the family Pospiviroidae. This element of secondary structure is formed by the upper CCR strand and a flanking inverted repeat of PSTVd, HSVd, CCCVd, ASSVd, and CbVd-1 (Coleus blumei viroid 1). Red fonts indicate conserved nucleotides in structurally similar positions. Continuous and broken lines represent Watson–Crick and non-canonical base-pairs, respectively. Notice that the variability preserves the overall structure of hairpin I, including the terminal palindromic tetraloop, the adjacent 3-bp stem, and the long stem. Left inset, hairpin I of the wild-type CEVd variant used to transform A. thaliana (notice two co-variations with respect to PSTVd at the basis of the long stem). Reproduced with permission from Gas et al. (2007).
Mentions: The metastable conformations contain hairpins, prominent among which is hairpin I (HP I) formed by the upper CCR strand and the flanking imperfect repeats. The finding that the nucleotide variability between members of the family Pospiviroidae preserves HP I (Riesner et al., 1979; Visvader et al., 1985; Polivka et al., 1996) – including the capping palindromic tetraloop with the two central residues phylogenetically conserved, the adjacent 3-bp stem with its central pair also phylogenetically conserved, an internal symmetric loop of 1–3 nt in each strand presumably stabilized by non-canonical interactions (Gast et al., 1998), and a stem of 9–10 bp occasionally interrupted by a 1-nt symmetric or asymmetric internal loop (Visvader et al., 1985; Flores et al., 1997; Figure 2) – adds further support to this structural element serving as the basis for an important function in vivo. In agreement with this notion, results obtained with an in vivo system based in transgenic Arabidopsis thaliana lines expressing dimeric transcripts of CEVd, Apple scar skin viroid (ASSVd), and Hop stunt viroid (HSVd) – that mimic the replicative intermediates – have mapped the cleavage site of the (+) strands of these three viroids at the upper CCR strand (Daròs and Flores, 2004; Gas et al., 2007), in a position homologous to that proposed for PSTVd with an in vitro system (Baumstark et al., 1997). Moreover, as a consequence of the peculiar features of HP I (Figure 2), the corresponding sequence of di- or oligomeric RNAs can alternative form a long double-stranded structure with a GC-rich central region of 10 bp containing the cleavage sites. The adoption in vivo of this double-stranded structure, which would be the actual substrate for cleavage in line with an early proposal (Diener, 1986), could be facilitated by hairpin I. More specifically, during transcription of oligomeric (+) RNAs of the family Pospiviroidae, a kissing-loop interaction between the palindromic tetraloops of two consecutive hairpin I motifs (Figure 3A), paralleling the situation observed in retroviruses (Paillart et al., 2004), might start intramolecular dimerization and their stems then form a longer interstrand duplex (Gas et al., 2007; Figure 3B). Furthermore, the cleavage sites in the double-stranded structure leave two 3′-protruding nucleotides in each strand (Figure 3C), the hallmark of class III RNases that display a clear preference for substrates with a compact secondary structure, like viroids, and generate products with 5′-phosphomonoester and free 3′-hydroxyl termini (MacRae and Doudna, 2007). The monomeric linear CEV (+) strands that accumulate in A. thaliana transgenically expressing the corresponding dimeric transcripts have indeed these termini (Gas et al., 2008), the ligation of which, interestingly, occurs through a novel pathway.

Bottom Line: As a consequence of two unique physical properties, small size and circularity, viroid RNAs do not code for proteins and thus depend on RNA sequence/structural motifs for interacting with host proteins that mediate their invasion, replication, spread, and circumvention of defensive barriers.Besides these most stable secondary structures, viroid RNAs alternatively adopt during replication transient metastable conformations containing elements of local higher-order structure, prominent among which are the hammerhead ribozymes catalyzing a key replicative step in the family Avsunviroidae, and certain conserved hairpins that also mediate replication steps in the family Pospiviroidae.Therefore, different RNA structures - either global or local - determine different functions, thus highlighting the need for in-depth structural studies on viroid RNAs.

View Article: PubMed Central - PubMed

Affiliation: Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC) Valencia, Spain.

ABSTRACT
As a consequence of two unique physical properties, small size and circularity, viroid RNAs do not code for proteins and thus depend on RNA sequence/structural motifs for interacting with host proteins that mediate their invasion, replication, spread, and circumvention of defensive barriers. Viroid genomes fold up on themselves adopting collapsed secondary structures wherein stretches of nucleotides stabilized by Watson-Crick pairs are flanked by apparently unstructured loops. However, compelling data show that they are instead stabilized by alternative non-canonical pairs and that specific loops in the rod-like secondary structure, characteristic of Potato spindle tuber viroid and most other members of the family Pospiviroidae, are critical for replication and systemic trafficking. In contrast, rather than folding into a rod-like secondary structure, most members of the family Avsunviroidae adopt multibranched conformations occasionally stabilized by kissing-loop interactions critical for viroid viability in vivo. Besides these most stable secondary structures, viroid RNAs alternatively adopt during replication transient metastable conformations containing elements of local higher-order structure, prominent among which are the hammerhead ribozymes catalyzing a key replicative step in the family Avsunviroidae, and certain conserved hairpins that also mediate replication steps in the family Pospiviroidae. Therefore, different RNA structures - either global or local - determine different functions, thus highlighting the need for in-depth structural studies on viroid RNAs.

No MeSH data available.


Related in: MedlinePlus